The new permit forms part of the final version of the US Fish & Wildlife Service (FWS)'s revised eagle management plan.
Independent contractors reporting to FWS will monitor the injuries or kills and the data will be made public. Previously, monitoring was self-reported and the data kept private.
The new eagle rule is to take effect on 15 January, just before Donald Trump takes office.
Wind companies — and all other companies that may unintentionally harm eagles — can apply for a permit.
The FWS estimates 4,200 bald and 2,000 golden eagles can be killed yearly, above current mortality rates, without the species declining.
For golden eagles, wind projects getting permits must provide a net conservation benefit to the species. Any groups that affect eagle numbers without a permit could face a penalty.
According to the American Wind Energy Association: "Studies show that wind energy is responsible for less than 3% of human-related deaths of golden eagles, and at over 90% of wind projects across the country there are no impacts on eagles at all."
In 2013, FWS approved a similar plan allowing 30-year permits, but a federal judge overturned it.
Trump's administration is expected to scrutinise wind turbine-bird kills more closely and could repeal the new rule, but doing so would take some time.
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